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<h1>Calculator Plugins</h1>

<h2>Introduction</h2>
<p>Calculator Plugins are modules of ChemAxon's Marvin and JChem
cheminformatics platforms which calculate physico-chemical properties from chemical structures. Calculator Plugins currently cover a range of
life science related properties and the development of new plugins is ongoing. 
Available directly from Marvin, Instant JChem and Reactor applications, command line, API or via ChemAxon's Chemical Terms language.</p>
<ul><li><p>In the graphical user interface of <b>MarvinSketch and MarvinView</b> the
      available calculator plugins are located in the <b class="buttonName">Tools</b>
  menu. The screenshots of this help were prepared using MarvinSketch v5.0.0 or above.</p></li>
  <li>
    <p>Plugin calculations can be run by the <b>command line tool cxcalc.</b>
      The calculations can be performed in single or batch mode. Batch processing is available using <a
        href="../applications/calc.html">Calculator</a> 
      (see the <a href="../applications/cxcalc-calculations.html">list of calculations</a>
      accessible from Calculator).
  </p></li>
  <li><p>The calculations are used in the <b>Chemical Terms</b> language with which you are
    able to calculate combinations of properties (like Lipinski's rule of 5) in
  an easy way. Learn more about it in the <a href="../chemicalterms/ChemicalTerms.html">Chemical Terms</a> section.</li>
  
  <li>
    <p>Plugin calculations can be used for filtering results of database searches 
      in <b>JChem Base, Instant JChem and JChem Cartridge</b>.
  </p></li>
  <li>
  <p>Define smart reaction rules using plugin calculations in <b>Reactor</b> (ChemAxon's virtual reaction processing tool).</p></li>
  <li>
    <p>Plugin calculations can be integrated easily into any <b>Java application.</b>  
      For more information on using calculator plugin Java API please see our
      <a href="http://www.chemaxon.com/marvin/help/developer/beans/api/index.html">
      chemaxon.marvin.calculation package</a>.
  </p></li>
  
</ul>



<h3>Contents</h3>
<ul>
	<li><a href="elemanal.html">Elemental Analysis Plugin</a>
	<li><a href="iupacnaming.html">Naming Plugin</a>
	<li><a href="protonation.html">Protonation</a>
	<ul>
		<li><a href="protonation.html#pka">p<i>K</i><sub>a</sub> Plugin</a> <img src="images/trainable_small.png" width="20" height="18" alt="Calculation can be trained with measured data"/>
		<li><a href="protonation.html#ms">Major Microspecies Plugin</a>
		<li><a href="protonation.html#isopoint">Isoelectric Point Plugin</a>
	</ul>
    <li><a href="partitioning.html">Partitioning</a> 
        
	<ul>
		<li><a href="partitioning.html#logp">log<i>P</i> Plugin</a> <img src="images/trainable_small.png" width="20" height="18" alt="Calculation can be trained with measured data"/>
		<li><a href="partitioning.html#logd">log<i>D</i> Plugin</a>
	</ul>
        <li><a href="chargegroup.html">Charge</a>
	<ul>
		<li><a href="chargegroup.html#charge">Charge Plugin</a>
		<li><a href="chargegroup.html#polarizability">Polarizability Plugin</a>
		<li><a href="chargegroup.html#oen">Orbital Electronegativity Plugin</a>
	</ul>
	<li><a href="isomers.html">Isomers</a>
	<ul>
		<li><a href="isomers.html#tautomer">Tautomerization Plugin</a>
		<li><a href="isomers.html#stereoisomer">Stereoisomer Plugin</a>
	</ul>
	<li><a href="conformation.html">Conformation</a>
	<ul>
		<li><a href="conformation.html#conformer">Conformer Plugin</a>
		<li><a href="conformation.html#moldyn">Molecular Dynamics Plugin</a>
        <li><a href="conformation.html#align">3D Alignment Plugin</a>
	</ul>
	<li><a href="geometrygroup.html">Geometry</a>
	<ul>
		<li><a href="geometrygroup.html#topolanal">Topology Analysis Plugin</a>
		<li><a href="geometrygroup.html#geometry">Geometry Plugin</a>
		<li><a href="geometrygroup.html#TPSA">Polar Surface Area Plugin (2D)</a>
		<li><a href="geometrygroup.html#MSA">Molecular Surface Area Plugin (3D)</a>
		
	</ul>
        <li><a href="markush.html">Markush Enumeration Plugin</a></li>
	<li><a href="other.html">Other</a>
	<ul>
		<li><a href="other.html#HBDA">Hydrogen Bond Donor-Acceptor Plugin</a>
		<li><a href="other.html#huckel">Huckel Analysis Plugin</a>
		<li><a href="other.html#refractivity">Refractivity Plugin</a>
		<li><a href="other.html#resonance">Resonance Plugin</a>
		<li><a href="other.html#framework">Structural Frameworks Plugin</a>
	</ul>
        <li><a href="Validations.html">Test Results</a></li>
	<li><a href="references.html">References</a></li>
</ul>



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